Research workbench
Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 GP120 core and to 17B Fab
Analyse Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 GP120 core and to 17B Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KLC
- Type
- protein
- Length
- 1,230 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M4H2K1 Fab heavy chain; M4H2K1 Fab light chain; 17B Fab light chain; 17B Fab heavy chain…
- UniProt
- Q2N0S5
- Ligands
- NAG, BMA, MAN
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | M4H2K1 Fab heavy chain | protein | 222 | 9% helix, 48% strand | — |
| L | M4H2K1 Fab light chain | protein | 218 | 7% helix, 52% strand | — |
| C | 17B Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| D | 17B Fab heavy chain | protein | 227 | 9% helix, 52% strand | — |
| A | HIV-1 clade a BG505 GP120,HIV-1 clade a BG505 GP120 | protein | 349 | 15% helix, 34% strand | Q2N0S5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, H
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.69 | 0.97 | 18 | empty |
| 2 | 675 | 0.67 | 0.76 | 60 | empty |
| 3 | 477 | 0.60 | 0.75 | 52 | empty |
| 4 | 87 | 0.57 | 0.86 | 24 | empty |
| 5 | 86 | 0.55 | 0.85 | 21 | NAG |
Interfaces
6 interfaces between chains.
- H–L · 2115 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1921 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 603 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 603 Ų buried · 8 hydrogen bonds · protein-protein
- L–A · 272 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7KLC · Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 gp120 core and to 17b Fab · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2N0S5
- Elsewhere: RCSB PDB 7KLC · PDBe 7KLC · UniProt Q2N0S5
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